Proteome Software Company Profile

Mission

Proteome Software is committed to setting the industry standard in MS/MS analysis
with our proteomics and metabolomics software. Our team of developers and technical
support specialists work together to bring you the most intuitive, highest-quality
products possible. From diligent programming and internal problem-solving to specific,
clear customer support and product documentation, our dedicated employees work every
day to create a satisfying user experience.

Scaffold

Where did the name Scaffold come from?

You may wonder where the name 'Scaffold' came from.
In construction, scaffolding can be a temporary structure for holding workers
and materials during the erection, repair, or decoration of a building.
In education, teachers use the concept of scaffolding to move students
beyond their current developmental stage or skill set and into progressively
more difficult tasks.

In the context of proteomics, Scaffold was envisioned to
compose a structure around the data so researchers have a flexible framework
that would simplify their analyses. The goal was software that is intuitive
and easy to use, built with powerful data manipulation that uses robust,
computationally-demanding statistics and automatic data recalculation
based on confidence thresholds. Scaffold was one of the first products to
offer a free viewer. This capability enables researchers to share their
results with colleagues. Empowering researchers and helping to further
scientific advances brings us all a huge source of pride and satisfaction.

Elements

Large-scale metabolomics experiments

Elements employs parallel processing to efficiently analyze hundreds of MS
samples with or without MS2 spectra. Metabolites are identified using multidimensional
search and scoring algorithms.

Select a level of summarization and create filtered, interactive heat maps.
Analyze complex experiments by using metadata to flexibly categorize your samples.
Organize and re-organize data for fast visualization and quantitative analyses.
Test for differential expression and calculate fold changes between samples and
categories based on signal intensity.

About Us

MS/MS analytics software

Proteome Software is a veteran-owned, scientist-operated small business located in Portland,
Oregon, USA. Here, we provide the MS/MS analytics community with an intuitive group of
proteomics and metabolomics tools. We use robust statistics to enable confident identification,
verification, and quantitation, working with researchers and other bioinformatics developers
to continuously revise our algorithms and support new workflows

Our customers drive us forward with their passion for doing their analytics right.
In return, we strive to make pursuing those passions easier. Our software analyzes complex
data with sound techniques that would be computationally difficult by other means.
Our resellers around the world reach a diverse group of laboratories in the commercial
and academic communities. We also distribute several other excellent products to support
your bioinformatics needs.

History

From an idea to a powerful analytical tool

In the spring of 2004, scientists Mark Turner, Brian Searle, and Ashley McCormack
came together with an idea.

They each knew the informatics problems that faced the proteomics community.
There were miles of Excel spreadsheets full of data, multiple search engines with
no way of combining results, and repetitive and exhausting analytical practices.
At the NIH/NIST Peptide Fragmentation Workshop in 2004, Brian and Mark heard all these
problems mapped out during a presentation by David Tabb. That night, they sat in their
hotel room and brainstormed solutions, motivated to improve the field of proteomics.

They brought their discussions back to their colleague and several months later, the three
of them developed what would soon become Proteome Software’s flagship product, Scaffold.

Proteome Software debuted Scaffold at the 2005 ASMS conference. Members of the proteomics
community were intrigued by Scaffold’s capability to combine multiple search engines’
results into a single analysis, inclusion of Peptide and Protein Prophet algorithms and
Tabb's user-selectable filter concept (DTA select).

Since then, Proteome Software had developed several landmark products, including launching
their first Metabolomics software tool, Elements, in 2015. Today, researchers and core
labs around the world have learned to rely on Proteome Software for performing complex
MS/MS analytics. Today, we continue to push our technologies into – and through – the
boundaries of biological examination.